deeptools_plot_pca: deepTools_macros.xml annotate

annotate deepTools_macros.xml @ 12:814bea57a4fe draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

author	bgruening
date	Fri, 31 Mar 2017 09:28:03 -0400
parents	fc06f0b21c23
children	dfe535b75616

rev	line source
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	1 <macros>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	2
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	4 <token name="@WRAPPER_VERSION@">2.5.0</token>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	5 <xml name="requirements">
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	6 <requirements>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	7 <requirement type="package" version="2.7.10">python</requirement>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	8 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	9 <yield />
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	10 </requirements>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	11 <expand macro="stdio" />
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	12 <version_command>@BINARY@ --version</version_command>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	13 </xml>
814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	14
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	15 <xml name="advancedOpt_scaffold">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	16 <conditional name="advancedOpt">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	18 <option value="no" selected="true">no</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	19 <option value="yes">yes</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	20 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	21 <when value="no" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	22 <when value="yes">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	23 <yield/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	24 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	25 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	26 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	27
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	28 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	29 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	30 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	31 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	32 --extendReads
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	33 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	34 $advancedOpt.ignoreDuplicates
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	35 $advancedOpt.centerReads
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	36 #if $advancedOpt.minMappingQuality:
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	37 --minMappingQuality '$advancedOpt.minMappingQuality'
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	38 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	39 #if $advancedOpt.samFlagInclude:
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	40 --samFlagInclude $advancedOpt.samFlagInclude
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	41 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	42 #if $advancedOpt.samFlagExclude:
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	43 --samFlagExclude $advancedOpt.samFlagExclude
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	44 #end if
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	45 #if $advancedOpt.minFragmentLength:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	46 --minFragmentLength $advancedOpt.minFragmentLength
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	47 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	48 #if $advancedOpt.maxFragmentLength:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	49 --maxFragmentLength $advancedOpt.maxFragmentLength
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	50 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	51 </token>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	52
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	53 <token name="@ADVANCED_OPTS_GTF@">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	54 $advancedOpt.metagene
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	55 #if $advancedOpt.transcriptID:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	56 --transcriptID $advancedOpt.transcriptID
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	57 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	58 #if $advancedOpt.exonID:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	59 --exonID $advancedOpt.exonID
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	60 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	61 #if $advancedOpt.transcript_id_designator:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	62 --transcript_id_designator $advancedOpt.transcript_id_designator
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	63 #end if
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	64 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	65
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	66 <xml name="heatmap_options">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	67 <expand macro="zMin_zMax" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	68 <expand macro="colorMap" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	69 <expand macro="plotTitle" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	70 <expand macro="plotNumbers" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	71 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	72
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	73 <token name="@HEATMAP_OPTIONS@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	74 #if str($plotting_type.zMin) != "":
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	75 --zMin $plotting_type.zMin
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	76 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	77 #if str($plotting_type.zMax) != "":
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	78 --zMax $plotting_type.zMax
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	79 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	80 --colorMap '$plotting_type.colorMap'
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	81 $plotting_type.plotNumbers
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	82 --plotTitle '$plotting_type.plotTitle'
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	83 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	84
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	85
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	86 <xml name="includeZeros">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	87 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	88 label="Include zeros"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	89 help="If set, then regions with zero counts for all BAM files are included. The default behavior is to ignore such regions." />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	90 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	91
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	92 <xml name="zMin_zMax">
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	93 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	94 help="If not specified the value is set automatically."/>
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	95 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	96 help="If not specified the value is set automatically."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	97 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	98
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	99 <xml name="region_limit_operation">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	100 <param argument="--region" type="text" value=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	101 label="Region of the genome to limit the operation to"
6 be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	102 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".">
be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	103 <sanitizer>
be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	104 <valid initial="string.letters,string.digits">
be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	105 <add value="\|"/>
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	106 <add value=":"/>
6 be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	107 </valid>
be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	108 </sanitizer>
be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	109 </param>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	110 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	111
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	112 <xml name="smoothLength">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	114 label="Smooth values using the following length (in bases)"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	115 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	116 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	117
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	118
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	119 <xml name="kmeans_clustering">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	120 <conditional name="used_multiple_regions">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	121 <param name="used_multiple_regions_options" type="select"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	122 label="Did you compute the matrix with more than one groups of regions?"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	123 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	124 <option value="yes">Yes, I used multiple groups of regions</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	125 <option value="no">No, I used only one group</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	126 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	127 <when value="no">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	128 <conditional name="clustering">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	129 <param name="clustering_options" type="select" label="Clustering algorithm">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	130 <option value="none">No clustering</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	131 <option value="kmeans">Kmeans clustering</option>
1 47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	132 <option value="hclust">Hierarchical clustering</option>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	133 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	134 <when value="kmeans">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	135 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	136 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	137 This only works for data that is not grouped, otherwise only the first group will be clustered.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	138 If more specific clustering methods are required it is advisable to save the underlying matrix and
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	139 run the clustering using other software."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	140 </when>
1 47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	141 <when value="hclust">
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	142 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	143 help="WARNING: This option causes the tool to run for a very long time! When this option is
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	144 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	145 This only works for data that is not grouped, otherwise only the first group will be clustered.
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	146 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	147 If more specific clustering methods are required it is advisable to save the underlying matrix and
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	148 run the clustering using other software."/>
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	149 </when>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	150 <when value="none" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	151 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	152 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	153 <when value="yes" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	154 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	155 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	156
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	157 <token name="@KMEANS_CLUSTERING@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	158 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	159 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	160 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	161 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	162 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	163 #end if
1 47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	164 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	165 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	166 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	167 #end if
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	168 #end if
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	169 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	170 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	171
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	172 <xml name="samFlags">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	173 <param argument="--samFlagInclude" type="integer" optional="True" value=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	174 label="Include reads based on the SAM flag"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	175 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	177 label="Exclude reads based on the SAM flag"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	178 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	179 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	180
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	181 <xml name="fragLength">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	183 label="Minimum fragment length for inclusion."
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	184 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	186 label="Maximum fragment length for inclusion."
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	187 help="A value of 0 (the default) is equivalent to no maximum." />
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	188 </xml>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	189
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	190 <xml name="read_processing_options">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	191 <expand macro="extendReads" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	192 <expand macro="ignoreDuplicates" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	193 <expand macro="centerReads" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	194 <expand macro="minMappingQuality" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	195 <expand macro="samFlags" />
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	196 <expand macro="fragLength" />
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	197 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	198
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	199 <xml name="gtf_options">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	201 label="Use a metagene model"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	202 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	204 label="trascript designator"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	205 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	206 <param argument="--exonID" optional="True" value="exon" type="text"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	207 label="exon designator"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	208 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	210 label="transcriptID key designator"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	211 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	212 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	215 </xml>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	216
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	217
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	218 <xml name="plotNumbers">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	220 label="Plot the correlation value"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	221 help="If set, then the correlation number is plotted on top of the heatmap."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	222 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	223
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	224 <xml name="extendReads">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	225 <conditional name="doExtendCustom">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	226 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	227 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	228 By default each read mate is extended.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	229 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	230 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	231 Reads are only extended if --extendReads is set to a value greater than the read length. NOTE: For spliced-read data, this option is not
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	232 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	233 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	234 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	235 <option value="custom">A custom length, which will be applied to ALL reads.</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	236 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	237 <when value="no" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	238 <when value="yes" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	239 <when value="custom">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	240 <param name="extendReadsValue" type="integer" value="300" min="1"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	241 label="Extend reads to the given average fragment size"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	242 help="Extend all reads to this length" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	243 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	244 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	245 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	246
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	247 <xml name="corMethod">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	248 <param argument="--corMethod" type="select" label="Correlation method">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	249 <option value="spearman" selected="True">Spearman</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	250 <option value="pearson">Pearson</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	251 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	252 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	253
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	254 <xml name="distanceBetweenBins">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	255 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	256 label="Distance between bins"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	257 help="By default, multiBamSummary considers consecutive bins of
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	258 the specified 'Bin size'. However, to reduce the
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	259 computation time, a larger distance between bins can
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	260 be given. Larger distances result in fewer bins being
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	261 considered."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	262 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	263
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	264 <xml name="centerReads">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	265 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	266 label="Center regions with respect to the fragment length"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	267 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	268 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	269
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	270 <xml name="ignoreDuplicates">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	271 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	272 label="Ignore duplicates"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	273 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	274 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	275
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	276 <xml name="sortUsing">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	277 <param argument="--sortUsing" type="select" label="Method used for sorting"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	278 help="For each row the method is computed.">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	279 <option value="mean" selected="true">mean</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	280 <option value="median">median</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	281 <option value="min">min</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	282 <option value="max">max</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	283 <option value="sum">sum</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	284 <option value="region_length">region length</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	285 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	286 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	287
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	288 <xml name="sortRegionsComputeMatrix">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	289 <param argument="--sortRegions" type="select" label="Sort regions"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	290 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	291 <option value="no">no ordering</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	293 <option value="descend">descending order</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	294 <option value="ascend">ascending order</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	295 </param>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	296 </xml>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	297
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	298 <xml name="sortRegions">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	299 <param argument="--sortRegions" type="select" label="Sort regions"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	300 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	301 <option value="no">no ordering</option>
11 fc06f0b21c23 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 10 diff changeset	302 <option value="descend" selected="true">descending order</option>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	303 <option value="ascend">ascending order</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	304 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	305 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	306
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	307 <xml name="minMappingQuality">
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	308 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	309 label="Minimum mapping quality"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	310 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	311 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	312
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	313 <xml name="skipZeros">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	314 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	315 label ="Skip zeros"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	316 help ="If set, then zero counts that happen for all BAM files given are ignored. This may result in fewer considered regions." />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	317 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	318
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	319 <xml name="fragmentLength">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	320 <param argument="--fragmentLength" type="integer" value="300" min="1"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	321 label="Fragment length used for the sequencing"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	322 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	323 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	324
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	325 <xml name="scaleFactor">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	327 help="The computed scaling factor will be multiplied by this (default 1)." />
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	328 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	329
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	330 <xml name="scaleFactors">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	331 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	332 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	333 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	334
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	335 <xml name="stdio">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	336 <stdio>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	337 <exit_code range="1:" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	338 <exit_code range=":-1" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	339 <regex match="Error:" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	340 <regex match="Exception:" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	341 <regex match="EXception:" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	342 <regex match="Traceback" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	343 </stdio>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	344 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	345
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	346 <xml name="pseudocount">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	347 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	348 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	349
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	350 <token name="@REFERENCES@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	351
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	352 .. class:: infomark
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	353
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	354 For more information on the tools, please visit our `help site`_.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	355
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	356 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	357
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	358 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	359
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	360 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	361 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	362 .. _help site: https://deeptools.readthedocs.org/
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	363
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	364 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	365 <xml name="citations">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	366 <citations>
6 be924b6a79ea planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty bgruening parents: 5 diff changeset	367 <citation type="doi">10.1093/nar/gkw257</citation>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	368 <yield />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	369 </citations>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	370 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	371
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	372 <xml name="multiple_input_bams">
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	373 <conditional name="multibam_conditional">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	374 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	375 <option value="No" selected="true">No</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	376 <option value="Yes">Yes</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	377 </param>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	378 <when value="No">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	379 <param argument="--bamfiles" type="data" format="bam" min="1"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	380 label="Bam file" multiple="true"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	381 help=""/>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	382 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	383 <when value="Yes">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	384 <repeat name="multibam_repeats" min="1" title="BAM Files">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	385 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	386 </repeat>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	387 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	388 </conditional>
1 47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	389 </xml>
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	390
47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	391 <xml name="multiple_input_bams_min2">
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	392 <conditional name="multibam_conditional">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	393 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	394 is vital to you, select Yes below.">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	395 <option value="No" selected="true">No</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	396 <option value="Yes">Yes</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	397 </param>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	398 <when value="No">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	399 <param argument="--bamfiles" type="data" format="bam" min="2"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	400 label="Bam file" multiple="true"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	401 help=""/>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	402 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	403 <when value="Yes">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	404 <repeat name="multibam_repeats" min="2" title="BAM Files">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	405 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	406 </repeat>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	407 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	408 </conditional>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	409 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	410
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	411 <xml name="multiple_input_bigwigs">
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	412 <conditional name="multibigwig_conditional">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	413 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	414 is vital to you, select Yes below.">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	415 <option value="No" selected="true">No</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	416 <option value="Yes">Yes</option>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	417 </param>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	418 <when value="No">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	419 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	420 label="Bigwig file"
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	421 help="A Bigwig file."/>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	422 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	423 <when value="Yes">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	424 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	425 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	426 </repeat>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	427 </when>
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	428 </conditional>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	429 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	430
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	431 <xml name="plotTitle">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	432 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	433 label="Title of the plot"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	434 help="Title of the plot, to be printed on top of the generated image." />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	435 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	436
1 47bf2e1f065b planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 bgruening parents: 0 diff changeset	437
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	438 <token name="@multiple_input_bams@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	439 <![CDATA[
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	440 #set files=[]
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	441 #set labels=[]
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	442 #import re
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	443 #if $multibam_conditional.orderMatters == "No":
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	446 ln -s "${bamfile}" "./${counter}.bam" &&
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	448 #silent $files.append('%s.bam' % $counter)
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	449 #silent $labels.append("'%s'" % identifier)
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	450 #end for
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	451 #else:
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	453 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
11 fc06f0b21c23 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 10 diff changeset	454 ln -s "${f.bamfiles}" "./${counter}.bam" &&
fc06f0b21c23 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 10 diff changeset	455 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	456 #silent $files.append('%s.bam' % $counter)
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	457 #silent $labels.append("'%s'" % $identifier)
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	458 #end for
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	459 #end if
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	460 ]]>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	461 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	462
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	463 <token name="@multiple_input_bigwigs@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	464 <![CDATA[
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	465 #set files=[]
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	466 #set labels=[]
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	467 #import re
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	468 #if $multibigwig_conditional.orderMatters == "No":
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	469 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	470 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	471 ln -s "${bigwig}" "${counter}.bw" &&
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	472 #silent $files.append('%s.bw' % $counter)
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	473 #silent $labels.append("'%s'" % $identifier)
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	474 #end for
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	475 #else:
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	476 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	477 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
11 fc06f0b21c23 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca bgruening parents: 10 diff changeset	478 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	479 #silent $files.append('%s.bw' % $counter)
12 814bea57a4fe planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 bgruening parents: 11 diff changeset	480 #silent $labels.append("'%s'" % $identifier)
10 21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	481 #end for
21b1f17dd208 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 bgruening parents: 9 diff changeset	482 #end if
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	483 ]]>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	484 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	485
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	486 <xml name="blacklist">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	487 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	488 label="Blacklisted regions in BED/GTF format"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	489 help="One or more files containing regions to exclude from the analysis" />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	490 </xml>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	491
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	492 <token name="@blacklist@">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	493 <![CDATA[
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	494 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	495 #set blfiles=[]
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	496 #for $f in $advancedOpt.blackListFileName:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	497 #silent $blfiles.append("'%s'" % $f)
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	498 #end for
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	499 #if $blfiles != ["'None'"]:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	500 --blackListFileName #echo ' '.join($blfiles)#
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	501 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	502 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	503 ]]>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	504 </token>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	505
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	506 <xml name="multiple_bed">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	507 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	508 label="Regions in BED/GTF format"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	509 help="One or more files containing regions to include in the analysis" />
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	510 </xml>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	511
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	512 <token name="@multiple_bed@">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	513 <![CDATA[
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	514 #set files=[]
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	515 #set labels=[]
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	516 #for $f in $BED:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	517 #silent $files.append("'%s'" % $f)
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	518 #silent $labels.append("'%s'" % $f.display_name)
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	519 #end for
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	520 #if len($files) > 0:
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	521 --BED #echo ' '.join($files)#
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	522 --regionLabels #echo ' '.join($labels)#
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	523 #end if
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	524 ]]>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	525 </token>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	526
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	527 <xml name="reference_genome_source">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	528 <conditional name="source">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	529 <param name="ref_source" type="select" label="Reference genome">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	530 <option value="cached">locally cached</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	531 <option value="history">in your history</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	532 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	533 <when value="cached">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	534 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	535 <options from_data_table="lastz_seqs">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	536 <filter type="sort_by" column="1" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	537 <validator type="no_options" message="No indexes are available." />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	538 </options>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	539 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	540 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	541 <when value="history">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	542 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	543 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	544 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	545 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	546
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	547 <token name="@reference_genome_source@">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	548 #if $source.ref_source=="history":
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	549 --genome $source.input1
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	550 #else:
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	551 --genome "$source.input1_2bit.fields.path"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	552 #end if
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	553 </token>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	554
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	555 <xml name="effectiveGenomeSize">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	556 <conditional name="effectiveGenomeSize">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	557 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	558 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	559 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	560 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	561 <option value="93260000">ce10 (93260000)</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	562 <option value="121400000">dm3 (121400000)</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	563 <option value="2451960000" selected="true">hg19 (2451960000)</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	564 <option value="2150570000">mm9 (2150570000)</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	565 <option value="specific">user specified</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	566 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	567 <when value="specific">
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	568 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	569 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	570 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	571 <when value="2150570000" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	572 <when value="2451960000" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	573 <when value="121400000" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	574 <when value="93260000" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	575 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	576 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	577
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	578 <xml name="skipNAs">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	579 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	580 label="Ignore missing data?"
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	581 help="This parameter determines if non-covered regions
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	582 (regions without overlapping reads) in a bam/bigWig file
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	583 should be skipped. The default is to treat those
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	584 regions as having a value of zero. The decision to
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	585 skip non-covered regions depends on the interpretation
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	586 of the data. Non-covered regions may represent, for
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	587 example, repetitive regions that should be ignored.
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	588 (default: False)" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	589 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	590
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	591 <xml name="input_save_matrix_values">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	592 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	593 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	594
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	595 <xml name="input_graphic_output_settings">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	596 <conditional name="output" >
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	597 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	598 <option value="no" selected="true">no</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	599 <option value="yes">yes</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	600 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	601 <when value="no" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	602 <when value="yes">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	603 <yield />
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	604 <param name="saveSortedRegions" type="boolean"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	605 label="Save the regions after skipping zeros or min/max threshold values"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	606 help="The order of the regions in the file follows the sorting order selected. This is useful,
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	607 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	608 </when>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	609 </conditional>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	610 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	611
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	612
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	613 <xml name="input_image_file_format">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	614 <param argument="--outFileFormat" type="select" label="Image file format">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	615 <option value="png" selected="true">png</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	616 <option value="pdf">pdf</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	617 <option value="svg">svg</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	618 <option value="eps">eps</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	619 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	620 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	621
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	622 <xml name="output_dpi">
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	623 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	624 label="Image dpi" help=""/>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	625 </xml>
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	626
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	627 <xml name="output_image_file_format">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	628 <data format="png" name="outFileName" label="${tool.name} image">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	629 <change_format>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	630 <when input="output.outFileFormat" value="pdf" format="pdf" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	631 <when input="output.outFileFormat" value="svg" format="svg" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	632 <when input="output.outFileFormat" value="eps" format="eps" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	633 </change_format>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	634 </data>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	635 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	636
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	637 <xml name="output_image_file_format_not_nested">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	638 <data format="png" name="outFileName" label="${tool.name} image">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	639 <change_format>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	640 <when input="outFileFormat" value="pdf" format="pdf" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	641 <when input="outFileFormat" value="svg" format="svg" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	642 <when input="outFileFormat" value="eps" format="eps" />
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	643 </change_format>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	644 </data>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	645 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	646
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	647 <xml name="output_save_matrix_values">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	648 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	649 <filter>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	650 ((
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	651 output['showOutputSettings'] == 'yes' and
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	652 output['saveMatrix'] is True
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	653 ))
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	654 </filter>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	655 </data>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	656 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	657
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	658 <xml name="output_graphic_outputs">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	659 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	660 <filter>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	661 ((
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	662 output['showOutputSettings'] == 'yes' and
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	663 output['saveSortedRegions'] is True
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	664 ))
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	665 </filter>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	666 </data>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	667 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	668
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	669 <xml name="colorMap">
8 1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	670 <param name="colorMap" type="select" label="Color map to use for the heatmap"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	671 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
1bd89a520120 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe bgruening parents: 7 diff changeset	672 multiple="true">
0 7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	673 <option value="RdYlBu" selected="true">RdYlBu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	674 <option value="Accent">Accent</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	675 <option value="Spectral">Spectral</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	676 <option value="Set1">Set1</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	677 <option value="Set2">Set2</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	678 <option value="Set3">Set3</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	679 <option value="Dark2">Dark2</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	680 <option value="Reds">Reds</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	681 <option value="Oranges">Oranges</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	682 <option value="Greens">Greens</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	683 <option value="Blues">Blues</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	684 <option value="Greys">Greys</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	685 <option value="Purples">Purples</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	686 <option value="Paired">Paired</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	687 <option value="Pastel1">Pastel1</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	688 <option value="Pastel2">Pastel2</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	689 <option value="spring">spring</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	690 <option value="summer">summer</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	691 <option value="autumn">autumn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	692 <option value="winter">winter</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	693 <option value="hot">hot</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	694 <option value="coolwarm">coolwarm</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	695 <option value="cool">cool</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	696 <option value="seismic">seismic</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	697 <option value="terrain">terrain</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	698 <option value="ocean">ocean</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	699 <option value="rainbow">rainbow</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	700 <option value="bone">bone</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	701 <option value="flag">flag</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	702 <option value="prism">prism</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	703 <option value="cubehelix">cubehelix</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	704 <option value="binary">binary</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	705 <option value="pink">pink</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	706 <option value="gray">gray</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	707 <option value="copper">copper</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	708 <option value="BrBG">BrBG</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	709 <option value="BuGn">BuGn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	710 <option value="BuPu">BuPu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	711 <option value="GnBu">GnBu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	712 <option value="OrRd">OrRd</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	713 <option value="PiYG">PiYG</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	714 <option value="PRGn">PRGn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	715 <option value="PuOr">PuOr</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	716 <option value="PuRd">PuRd</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	717 <option value="PuBu">PuBu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	718 <option value="RdBu">RdBu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	719 <option value="RdGy">RdGy</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	720 <option value="RdPu">RdPu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	721 <option value="YlGn">YlGn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	722 <option value="PuBuGn">PuBuGn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	723 <option value="RdYlGn">RdYlGn</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	724 <option value="YlGnBu">YlGnBu</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	725 <option value="YlOrBr">YlOrBr</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	726 <option value="YlOrRd">YlOrRd</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	727 <option value="gist_gray">gist_gray</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	728 <option value="gist_stern">gist_stern</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	729 <option value="gist_earth">gist_earth</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	730 <option value="gist_yarg">gist_yarg</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	731 <option value="gist_ncar">gist_ncar</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	732 <option value="gist_rainbow">gist_rainbow</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	733 <option value="gist_heat">gist_heat</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	734 <option value="gnuplot">gnuplot</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	735 <option value="gnuplot2">gnuplot2</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	736 <option value="CMRmap">CMRmap</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	737 <option value="bwr">bwr</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	738 <option value="hsv">hsv</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	739 <option value="brg">brg</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	740 <option value="jet">jet</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	741 <option value="afmhot">afmhot</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	742 <option value="Accent_r">Accent reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	743 <option value="Spectral_r">Spectral reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	744 <option value="Set1_r">Set1 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	745 <option value="Set2_r">Set2 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	746 <option value="Set3_r">Set3 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	747 <option value="Dark2_r">Dark2 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	748 <option value="Reds_r">Reds reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	749 <option value="Oranges_r">Oranges reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	750 <option value="Greens_r">Greens reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	751 <option value="Blues_r">Blues reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	752 <option value="Greys_r">Greys reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	753 <option value="Purples_r">Purples reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	754 <option value="Paired_r">Paired reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	755 <option value="Pastel1_r">Pastel1 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	756 <option value="Pastel2_r">Pastel2 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	757 <option value="spring_r">spring reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	758 <option value="summer_r">summer reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	759 <option value="autumn_r">autumn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	760 <option value="winter_r">winter reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	761 <option value="hot_r">hot reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	762 <option value="coolwarm_r">coolwarm reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	763 <option value="cool_r">cool reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	764 <option value="seismic_r">seismic reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	765 <option value="terrain_r">terrain reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	766 <option value="ocean_r">ocean reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	767 <option value="rainbow_r">rainbow reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	768 <option value="bone_r">bone reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	769 <option value="flag_r">flag reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	770 <option value="prism_r">prism reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	771 <option value="cubehelix_r">cubehelix reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	772 <option value="binary_r">binary reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	773 <option value="pink_r">pink reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	774 <option value="gray_r">gray reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	775 <option value="copper_r">copper reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	776 <option value="BrBG_r">BrBG reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	777 <option value="BuGn_r">BuGn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	778 <option value="BuPu_r">BuPu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	779 <option value="GnBu_r">GnBu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	780 <option value="OrRd_r">OrRd reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	781 <option value="PiYG_r">PiYG reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	782 <option value="PRGn_r">PRGn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	783 <option value="PuOr_r">PuOr reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	784 <option value="PuRd_r">PuRd reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	785 <option value="PuBu_r">PuBu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	786 <option value="RdBu_r">RdBu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	787 <option value="RdGy_r">RdGy reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	788 <option value="RdPu_r">RdPu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	789 <option value="YlGn_r">YlGn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	790 <option value="PuBuGn_r">PuBuGn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	791 <option value="RdYlBu_r">RdYlBu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	792 <option value="RdYlGn_r">RdYlGn reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	793 <option value="YlGnBu_r">YlGnBu reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	794 <option value="YlOrBr_r">YlOrBr reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	795 <option value="YlOrRd_r">YlOrRd reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	796 <option value="gist_gray_r">gist_gray reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	797 <option value="gist_stern_r">gist_stern reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	798 <option value="gist_earth_r">gist_earth reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	799 <option value="gist_yarg_r">gist_yarg reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	800 <option value="gist_ncar_r">gist_ncar reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	801 <option value="gist_rainbow_r">gist_rainbow reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	802 <option value="gist_heat_r">gist_heat reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	803 <option value="gnuplot_r">gnuplot reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	804 <option value="gnuplot2_r">gnuplot2 reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	805 <option value="CMRmap_r">CMRmap reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	806 <option value="bwr_r">bwr reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	807 <option value="hsv_r">hsv reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	808 <option value="brg_r">brg reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	809 <option value="jet_r">jet reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	810 <option value="afmhot_r">afmhot reversed</option>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	811 </param>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	812
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	813 </xml>
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	814
7fb0a96e74c1 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty bgruening parents: diff changeset	815 </macros>

Mercurial > repos > bgruening > deeptools_plot_pca

annotate deepTools_macros.xml @ 12:814bea57a4fe draft